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= OBITools =
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'''OBITools''' is a set of python programs developed to simplify the manipulation of sequence files in our labs.
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They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina)
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in the context of [http://metabarcoding.org DNA Metabarcoding].
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They are highly related with the following softwares:
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- [http://www.grenoble.prabi.fr/trac/ecoPCR ecoPCR] for [http://metabarcoding.org DNA Metabarcoding] primers in silico evaluation.
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- [http://www.grenoble.prabi.fr/trac/ecoPrimers ecoPrimers] for [http://metabarcoding.org DNA Metabarcoding] primers design.
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- [http://metabarcoding.org/sumatra sumatra and sumaclust] for fast alignment and clustering of NGS reads.
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The programs evolved with our needs. They mainly provide facilities to manipulate sequence files in [http://en.wikipedia.org/wiki/FASTA_format Fasta] and
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[http://en.wikipedia.org/wiki/FASTQ_format FastQ] format. Other input formats like [http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html genbank]
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or [http://en.wikipedia.org/wiki/European_Nucleotide_Archive embl] are supported too as well as formats related to
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[http://www.grenoble.prabi.fr/trac/ecoPCR ecoPCR].
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== The '''OBITools''' programs ==
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The '''OBITools''' programs aims to help you to manipulate various data and sequence files in a convenient way using the
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''Unix'' command line interface.
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They follow the standard ''Unix'' interface for command line program, allowing to chain a set of commands
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using the pipe mecanism.
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All these programs have a {{{-h}}} option printing a small online help to describe the different options accepted by the programs.
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A complete documentation is available [http://metabarcoding.org/obitools/doc here]
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Most of the '''OBITools''' programs' names start by `obi`. By using the command autocompletion behavior of your unix shell you
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can have easily access to all the command name.
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== Some way to use '''obitools''' ==
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A complete tutorial, demonstrating how to analyse DNA metabarcoding data using '''OBITools''' is available [http://metabarcoding.org/obitools/doc here]
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== Download and install '''OBITools''' ==
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OBITools are deposed on the PYPI archive site, you can easily install them on your computer using the Python
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[http://pip.readthedocs.org/en/latest/installing.html pip] installer. We recommend the [http://pip.readthedocs.org/en/latest/installing.html pip]
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installer rather than the `easy_install` one as [http://pip.readthedocs.org/en/latest/installing.html pip] take in charge dependencies between
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python modules
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For a full description of the installation procedure, please consult the [http://metabarcoding.org/obitools/doc/wolves.html OBITools documentation]. |